RetrogeneDB ID: retro_cjac_2506

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:22930747..22931629(+)
• Located in intron of: ENSCJAG00000004853

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020635
• Aliases: None
• Description: ATP synthase gamma chain [Source:UniProtKB/TrEMBL;Acc:F7I4L8]

Sequence

>retro_cjac_2506
ATGTTCTCCGGCGCCGGCATCTCTGGGCTGTCGTCCTGGACCTTGCAGCTGCAATGGATTCAAGTTCGAAATATGGCAAC
TTTGAAAGATATTACCAGGTGACTAAAGTCCATCAAAAACATCCAGAAAATTACCGGGTCTATGAAAATGGTAGCAGCAG
CAAAATATGCCTGAGCTGAGAGAGAGCTGAAACCAGCTCGAATACACGGATTGGGATCTTTGGCTCTGTGTGAAAAAGCT
GATATCAAGACGCTTGAAGACAAGAAGAAACACCTTATTGGTGTGTCCTCAGATCAAGGACTGTGTGATGCTCTTCACTC
CTCCATTGCTAAACAGATGAAAAGCGAGGTTGCTACACTAACAGCAGCTGGGAAGGAAGTTATGCCTGTTGGAATTGGTG
ACAAAATCAGAGACATACTTTATAGGGCTCATTCTGACCAGTTTCTAGCGGCATTTAAAGAAGTAGGAAGAAAGCCCCCT
ACTTGTGGAGATGTGTCAGTCATTGCCCTTAAATTACTAAATTCTGGATATGAATTTGATGAAGGCTCCATCTTTAATGG
ATTCAGGTCTGTTTTCTCCTATAAGACAGAGGAAAAGCCCATCTTTTCCCTTAATACCGTTGCAAGTGCTGAGAGCATGA
GTATCTACGATGATATTGATGCTGATGTGCTGCACAATTACCAAGAATACAGTCTGGCCAACATCATCTACTACTCTCTG
AAGGAGTCCACCAGTGAGCAGAGCGCCAGGATGACAGCCATGGACAACGCCGGCAAGAATGCTTCTGAGATGATTGACAG
ATGGACATTGACATTCAACCGTTCCCTCCAAGCTGTCATCACAAAGGAGTTGATTGAAATCATCTCTGGTGCTGCAGCTC
TG

Alignment

ORF - retro_cjac_2506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFSRAGVSGLSAWTLQPQWIQVRNMATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARIYG
          MFS.AG.SGLS.WTLQ.QWIQVRNMATLKDITR.LKSIKNIQKIT.SMKMVAAAKYA.AERELKPARI.G
Retrocopy MFSGAGISGLSSWTLQLQWIQVRNMATLKDITR*LKSIKNIQKITGSMKMVAAAKYA*AERELKPARIHG

Parental  LGSLALYEKADIKGPEDKKKHLLIGVSSDRGLCGAIHSSIAKQMKSEVATLTAAGKEVMLVGIGDKIRGI
          LGSLAL.EKADIK..EDKKKHL.IGVSSD.GLC.A.HSSIAKQMKSEVATLTAAGKEVM.VGIGDKIR.I
Retrocopy LGSLALCEKADIKTLEDKKKHL-IGVSSDQGLCDALHSSIAKQMKSEVATLTAAGKEVMPVGIGDKIRDI

Parental  LYRTHSDQFLAAFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFSLNTIA
          LYR.HSDQFLAAFKEVGR.PPT.GD.SVIAL.LLNSGYEFDEGS.IFN.FRSV.SYKTEEKPIFSLNT.A
Retrocopy LYRAHSDQFLAAFKEVGRKPPTCGDVSVIALKLLNSGYEFDEGS-IFNGFRSVFSYKTEEKPIFSLNTVA

Parental  SAESMSIYDDIDADVLQNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTRQ
          SAESMSIYDDIDADVL.NYQEYSLANIIYYSLKES.TSEQSARMTAMDNA.KNASEMID..TLTFNR..Q
Retrocopy SAESMSIYDDIDADVLHNYQEYSLANIIYYSLKES-TSEQSARMTAMDNAGKNASEMIDRWTLTFNRSLQ

Parental  AVITKELIEIISGAAAL
          AVITKELIEIISGAAAL
Retrocopy AVITKELIEIISGAAAL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	39.45 RPM
SRP051959_heart	0.00 RPM	96.77 RPM
SRP051959_kidney	0.02 RPM	59.57 RPM
SRP051959_liver	0.00 RPM	49.73 RPM
SRP051959_lung	0.02 RPM	23.64 RPM
SRP051959_lymph_node	0.00 RPM	26.53 RPM
SRP051959_skeletal_muscle	0.00 RPM	95.56 RPM
SRP051959_spleen	0.00 RPM	23.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2506 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2506 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2506 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005024	1 retrocopy	retro_cfam_1781,
Choloepus hoffmanni	ENSCHOG00000011229	3 retrocopies	retro_chof_102, retro_chof_297, retro_chof_673,
Callithrix jacchus	ENSCJAG00000020635	7 retrocopies	retro_cjac_1079, retro_cjac_1293, retro_cjac_1381, retro_cjac_1636, retro_cjac_2506 , retro_cjac_4190, retro_cjac_526,
Cavia porcellus	ENSCPOG00000010523	2 retrocopies	retro_cpor_422, retro_cpor_984,
Echinops telfairi	ENSETEG00000010549	1 retrocopy	retro_etel_1406,
Felis catus	ENSFCAG00000000196	1 retrocopy	retro_fcat_818,
Homo sapiens	ENSG00000165629	1 retrocopy	retro_hsap_1415,
Gorilla gorilla	ENSGGOG00000009719	1 retrocopy	retro_ggor_1094,
Macaca mulatta	ENSMMUG00000009207	1 retrocopy	retro_mmul_2254,
Monodelphis domestica	ENSMODG00000016720	1 retrocopy	retro_mdom_1287,
Mus musculus	ENSMUSG00000025781	4 retrocopies	retro_mmus_1122, retro_mmus_2008, retro_mmus_3451, retro_mmus_3644,
Nomascus leucogenys	ENSNLEG00000011917	1 retrocopy	retro_nleu_1836,
Oryctolagus cuniculus	ENSOCUG00000004642	2 retrocopies	retro_ocun_1171, retro_ocun_363,
Otolemur garnettii	ENSOGAG00000015242	2 retrocopies	retro_ogar_1099, retro_ogar_2738,
Procavia capensis	ENSPCAG00000004971	1 retrocopy	retro_pcap_99,
Pongo abelii	ENSPPYG00000002076	1 retrocopy	retro_pabe_1170,
Pan troglodytes	ENSPTRG00000002277	1 retrocopy	retro_ptro_968,
Pteropus vampyrus	ENSPVAG00000006512	3 retrocopies	retro_pvam_1466, retro_pvam_51, retro_pvam_530,
Ictidomys tridecemlineatus	ENSSTOG00000026133	1 retrocopy	retro_itri_665,
Tupaia belangeri	ENSTBEG00000011530	4 retrocopies	retro_tbel_1763, retro_tbel_2023, retro_tbel_4384, retro_tbel_4406,
Tarsius syrichta	ENSTSYG00000003035	4 retrocopies	retro_tsyr_1268, retro_tsyr_1988, retro_tsyr_465, retro_tsyr_506,